GenomicReports {beadarraySNP} | R Documentation

## Genomic reports

### Description

Create reports for all samples in a dataset.

### Usage

    reportChromosomesSmoothCopyNumber(snpdata, grouping, normalizedTo=2,
      smooth.lambda=2, ridge.kappa=0, plotLOH=c("none", "marker", "line", "NorTum"),
      sample.colors = NULL, ideo.bleach=0.25, ...)
    reportSamplesSmoothCopyNumber(snpdata, grouping, normalizedTo=2,
      smooth.lambda=2, ridge.kappa=0, plotLOH=c("none", "marker", "line", "NorTum"),
      sample.colors=NULL, ...)
    reportGenomeGainLossLOH(snpdata, grouping, plotSampleNames=FALSE, sizeSampleNames=4,
      distance.min, upcolor="red", downcolor="blue", lohcolor="grey", hetcolor="lightgrey",
      lohwidth=1, segment=101, orientation=c("V","H"), ...)
    reportChromosomeGainLossLOH(snpdata, grouping, plotSampleNames=FALSE, distance.min,
      upcolor="red", downcolor="blue", lohcolor="grey", hetcolor="lightgrey", proportion=0.2,
      plotLOH=TRUE, segment=101, ...)
    reportGenomeIntensityPlot(snpdata, normalizedTo=NULL, subsample=NULL, smoothing=c("mean", "quant"),
      dot.col="black", smooth.col="red", ...)

### Arguments

`snpdata` | SnpSetIllumina object.
`grouping` | factor, elements with same value are plotted together. Defaults to groups of 4 in order of the samples in the object.
`normalizedTo` | numeric, a horizontal line is drawn at this position.
`smooth.lambda` | smoothing parameter for `quantsmooth`.
`ridge.kappa` | smoothing parameter for `quantsmooth`.
`plotLOH` | indicate regions or probes with LOH, see details.
`sample.colors` | vector of color.
`plotSampleNames` | logical.
`sizeSampleNames` | numeric, margin size for sample names.
`distance.min` | numerical.
`upcolor` | color.
`downcolor` | color.
`lohcolor` | color.
`hetcolor` | color.
`lohwidth` | numerical, relative width of the LOH part of the sample
`segment` | integer.
`orientation` | ["V","H"], vertical or horizontal orientation of plot.
`proportion` | numerical, proportion of the plot to use for idiogram annotation
`subsample` | character, or factor of length of features
`smoothing` | Type of smoothing per chromosome.
`dot.col` | color.
`smooth.col` | color.
`ideo.bleach` | numeric [0,1]
`...` | arguments are forwarded to `plot` or `getChangedRegions`.

### Details

The first function creates plots for each group and each chromosome in the dataset. The second function creates full genome plot for each group in the dataset. Beware that a lot of plots can be created, and usually you should prepare for that, by redirecting the plots to `pdf` or functions that create picture files like `jpg, png, bmp`.

### Value

These functions are executed for their side effects

### Author(s)

Jan Oosting

### See Also

`quantsmooth`,`prepareGenomePlot`, `pdfChromosomesSmoothCopyNumber`, `pdfSamplesSmoothCopyNumber`

### Examples

    data(chr17.260)
    chr17nrm <- standardNormalization(chr17.260)
    par(mfrow = c(4,2), mar = c(2,4,2,1))
    reportChromosomesSmoothCopyNumber(chr17nrm, grouping=pData(chr17.260)$Group,smooth.lambda = 4)

[Package beadarraySNP version 1.60.0 Index]